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charliefornia / TEchim

Tools to find TE-gene chimera
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TEchim_part2_mRNA.sh #3

Open WalterHK opened 3 years ago

WalterHK commented 3 years ago

Hello,

     Thank you for sharing this great tool for us to explore transposon in NGS data. Currently, I am using it to investigate TE in human RNAseq data. I enter a problem in the combine_hits_of_each_TE in the captioned sh file. I checked that out03a_uniqueTEs.tsv was successfully created, but all subsequent output file has zero data inside. Could you give me some hints what should I try to make this part work?

     Thank you.

Regards, Walter Yeung

     Following are the parameter I added in part1.sh and part2_mRNA.sh:

Part1: wd=/home/RNAseq/paired/TEchim_output/ # working directory SNa=normal
FASTQ1=/home/RNAseq/paired/paired_fq/normal_1_paired.fq.gz
FASTQ2=/home/RNAseq/paired/paired_fq/normal_2_paired.fq.gz
SNo=1
LNo=1
stranded=2
REFpath=/home/annotations/RNAseq/TEChim_ref/
nc=40
fastalength=58

Part2: wd=/home/RNAseq/paired/TEchim_part2
path_to_PART1_output=/homeRNAseq/paired/TEchim_output_part1/
SNa=normal nc=40
REFpath=/home/annotations/RNAseq/TEChim_ref/

charliefornia commented 3 years ago

Hi Walter, Many thanks for getting in touch. I'm super busy at the moment and I will get back to you as soon as possible. Many apologies for the delay. best regards, Charly.